Research workbench
Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient, polymorph 3
Analyse Cryo-EM structure of TMEM106B fibrils extracted from a ftld-tdp patient… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SAS
- Type
- protein
- Length
- 1,350 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein 106B
- UniProt
- Q9NUM4
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 0% helix, 79% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Transmembrane protein 106B | protein | 135 | 0% helix, 79% strand | Q9NUM4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, D, E, B, F, C, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.76 | 0.84 | 44 | empty |
| 2 | 349 | 0.76 | 0.87 | 38 | empty |
| 3 | 470 | 0.76 | 0.83 | 45 | empty |
| 4 | 683 | 0.76 | 0.81 | 47 | empty |
| 5 | 674 | 0.75 | 0.81 | 46 | empty |
Interfaces
23 interfaces between chains.
- B–C · 5940 Ų buried · 182 hydrogen bonds · protein-protein
- B–F · 5940 Ų buried · 182 hydrogen bonds · protein-protein
- C–G · 5940 Ų buried · 182 hydrogen bonds · protein-protein
- F–J · 5938 Ų buried · 182 hydrogen bonds · protein-protein
- D–H · 5925 Ų buried · 182 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SAS · Cryo-EM structure of TMEM106B fibrils extracted from a FTLD-TDP patient, polymorph 3 · the same entry in another collection · chain J against J, TM-score 1.00
- Q9NUM4 · AlphaFold monomer V2.0 prediction for transmembrane protein 106B (Q9NUM4) · a predicted model of the same protein · chain A against A, TM-score 0.22
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NUM4
- Elsewhere: RCSB PDB 7SAS · PDBe 7SAS · UniProt Q9NUM4
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